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Due to their documented epidemiological relevance as hosts for influenza A viruses (IAV), humans, poultry and pigs in backyard production systems (BPS) within wetlands could be key to the emergence of novel IAV variants able to transmit between humans or animals. To better understand the circulation of IAV at the human-animal interface of BPS within wetlands, we studied IAV in backyard duck flocks and pig herds in the Pacific Coast of Guatemala. From April 2013 to October 2014, we estimated the monthly IAV per cent seropositive and viral positive flocks and herds in two resource-limited communities. We detected antibodies in sera against the IAV nucleoprotein through ELISA. We also detected IAV viral RNA in respiratory (ducks and pigs) and cloacal (ducks) swabs through rRT-PCR directed at the matrix gene. We attempted viral isolation in eggs or MDCK cells followed by sequencing from swabs positive for IAV. During our study period, IAV seropositivity in duck flocks was 38%, and viral positivity was 23% (n = 86 BPS sampled). IAV seropositivity in pig herds was 42%, and viral positivity was 20% (n = 90 BPS sampled). Both flocks and herds had detectable antibodies against IAV mostly year-round, and IAV was detected in several months. We isolated an H3N2 virus from one pig sampled at the end of 2013. Standard nucleotide BLAST searches indicate that the isolated virus was similar to seasonal viruses circulating in humans, suggesting human-to-pig transmission. Our data show concurrent circulation of IAV in multiple species of poultry and pigs that were commingled in rudimentary conditions in proximity to humans, but no significant risk factors could be identified.

Waterfowl species are known to harbor the greatest diversity of low pathogenicity influenza A virus (LPAIV) subtypes and are recognized as their main natural reservoir. In Guatemala there is evidence of circulation of LPAIV in wild ducks; however, the bird species contributing to viral diversity during the winter migration in Central America are unknown. In this study, samples obtained from 1250 hunter-killed birds from 22 different species were collected on the Pacific coast of Guatemala during three winter migration seasons between 2010 and 2013. Prevalence of LPAIV detected by real-time reverse-transcriptase polymerase chain reaction was 38.2%, 23.5%, and 24.7% in the 2010-11, 2011-12, and 2012-13 seasons, respectively. The highest virus prevalence was detected in the northern shoveler (Anas clypeata), followed by the blue-winged teal (Anas discors). The majority of positive samples and viral isolates were obtained from the blue-winged teal. Analysis of LPAIV prevalence over time in this species indicated a decreasing trend in monthly prevalence within a migration season. Sixty-eight viruses were isolated, and nine HA and seven NA subtypes were identified in 19 subtype combinations. In 2012-13 the most prevalent subtype was H14, a subtype identified for the first time in the Western Hemisphere in 2010. The results from this study represent the most detailed description available to date of LPAIV circulation in Central America.

Recent outbreaks of highly pathogenic H7N3, H5Nx, and H7N8 avian influenza viruses in North America were introduced by migratory birds, underscoring the importance of understanding how wild birds contribute to the dissemination and evolution of IAVs in nature. At least four of the main IAV duck host species in North America migrate through or overwinter within a narrow strip of Central America, providing opportunities for diverse IAV lineages to mix and exchange gene segments. By obtaining whole-genome sequences of 68 IAV isolates collected from migratory waterfowl in Guatemala (2010 to 2013), the largest data set available from Central America to date, we detected extensive viral diversity, including gene variants rarely found in North America and gene segments of Eurasian origin. Our findings highlight the need for increased IAV surveillance across the geographical span of bird migration flyways, including Neotropical regions that have been vastly undersampled to date., Over a hundred species of aquatic birds overwinter in Central America’s wetlands, providing opportunities for the transmission of influenza A viruses (IAVs). To date, limited IAV surveillance in Central America hinders our understanding of the evolution and ecology of IAVs in migratory hosts within the Western Hemisphere. To address this gap, we sequenced the genomes of 68 virus isolates obtained from ducks overwintering along Guatemala’s Pacific Coast during 2010 to 2013. High genetic diversity was observed, including 9 hemagglutinin (HA) subtypes, 7 neuraminidase (NA) subtypes, and multiple avian IAV lineages that have been detected at low levels (

Seasonal dynamics of influenza A viruses (IAVs) are driven by host density and population immunity. Through an analysis of subtypic data for IAVs isolated from Blue-winged Teal (Anas discors), we present evidence for seasonal patterns in the relative abundance of viral subtypes in spring and summer/autumn.

Background Guatemala is the country with the largest swine production in Central America; however, evidence of influenza A virus (IAV) in pigs has not been clearly delineated. Objectives In this study, we analyzed the presence and spatial distribution of IAV in commercial and backyard swine populations. Methods Samples from two nation-wide surveys conducted in 2010 and 2011 were tested using virological (rRT-PCR and virus isolation) and serological (ELISA and Hemagglutination Inhibition) assays to detect IAV. Results IAV was detected in 15.7% of the sampled pigs (30.6% of herds) in 2010 and in 11.7% (24.2% of herds) in 2011. The percentage of seropositive pigs was 10.6% (16.1% of herds) and 1.4% (3.1% of herds) for each year respectively. Three pandemic H1N1 and one seasonal human-like H3N2 viruses were isolated. Antibodies against viruses from different genetic clusters were detected. No reassortant strains with swine viruses were detected. The H3N2 virus was closely related to human viruses that circulated in Central America in 2010, distinct to the most recent human seasonal vaccine lineages. Spatial clusters of rRT-PCR positive herds were detected each year by scan statistics. Conclusions Our results demonstrate circulation of IAV throughout Guatemala, and identify commercial farms, animal health status and age as potential risk factors associated to IAV infection and exposure. Detection of human-origin viruses in pigs suggests a role for humans in the molecular epidemiology of IAV in swine in Guatemala and evidences gaps in local animal and human surveillance. This article is protected by copyright. All rights reserved.

West Nile virus ecology has yet to be rigorously investigated in the Caribbean Basin. We identified a transmission focus in Puerto Barrios, Guatemala, and established systematic monitoring of avian abundance and infection, seroconversions in domestic poultry, and viral infections in mosquitoes. West Nile virus transmission was detected annually between May and October from 2005 to 2008. High temperature and low rainfall enhanced the probability of chicken seroconversions, which occurred in both urban and rural sites. West Nile virus was isolated from Culex quinquefasciatus and to a lesser extent, from Culex mollis/Culex inflictus, but not from the most abundant Culex mosquito, Culex nigripalpus. A calculation that combined avian abundance, seroprevalence, and vertebrate reservoir competence suggested that great-tailed grackle (Quiscalus mexicanus) is the major amplifying host in this ecosystem. West Nile virus transmission reached moderate levels in sentinel chickens during 2007, but less than that observed during outbreaks of human disease attributed to West Nile virus in the United States.

The role wild bird species play in the transmission and ecology of avian influenza virus (AIV) is well established; however, there are significant gaps in our understanding of the worldwide distribution of these viruses, specifically about the prevalence and/or significance of AIV in Central and South America. As part of an assessment of the ecology of AIV in Guatemala, we conducted active surveillance in wild birds on the Pacific and Atlantic coasts. Cloacal and tracheal swab samples taken from resident and migratory wild birds were collected from February 2007 to January 2010.1913 samples were collected and virus was detected by real time RT-PCR (rRT-PCR) in 28 swab samples from ducks (Anas discors). Virus isolation was attempted for these positive samples, and 15 isolates were obtained from the migratory duck species Blue-winged teal. The subtypes identified included H7N9, H11N2, H3N8, H5N3, H8N4, and H5N4. Phylogenetic analysis of the viral sequences revealed that AIV isolates are highly similar to viruses from the North American lineage suggesting that bird migration dictates the ecology of these viruses in the Guatemalan bird population.